Abstract

It is well known that synthetic gene expression is
highly sensitive to how genetic elements (promoter
structure, spacing regions between promoter and cod-
ing sequences, ribosome binding sites, etc.) are spatially
configured. An important topic that has received far less
attention is how the compositional context, or spatial
arrangement, of entire genes within a synthetic gene
network affects their individual expression levels. In this
paper we show, both quantitatively and qualitatively, that
compositional context significantly alters transcription
levels in synthetic gene networks. We demonstrate
that key characteristics of gene induction, such as
ultra-sensitivity and dynamic range, strongly depend on
compositional context. We postulate that supercoiling
can be used to explain this interference and validate
this hypothesis through modeling and a series of in
vitro supercoiling relaxation experiments. This compo-
sitional interference enables a novel form of feedback
in synthetic gene networks. We illustrate the use of this
feedback by redesigning the toggle switch to incorporate
compositional context. We show the context-optimized
toggle switch has improved threshold detection and
memory properties.